RetrogeneDB ID:

retro_lafr_790

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_39:1368989..1370663(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSLAFG00000030312
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_790
ATGCCTAAGAGACCTGCAGTTGGCATTGATCTTGGCACCATCTACTCCCATGTGGGTGTCTTCCAGCTAGGGAAAGTGGA
GATAATTGCAAATGATCAGGGCAACCGAACCACCCCAAGCTATACCTCTTTTATTGATATTGAGTGATTGATCGGTGATG
CCAGAAAGAACCAAGTTGCGATGAATCCCACTAACACTGTTTTTGATGCCAAATGTCTGACTGGATAAAGATTTGATGAT
GCTGTTGTCCAGTCTGATATGAAGTATTGGCCCTTCATGGAGTAGAGTGATGCAGGCAGACCCAAGGTCCAAATAGAATA
TAAGGATAAGGGAGAGACCAAAAGTTTCTATCCAGAGGAGGTGTCATCTATGGTTCTGACGAAGATGAAGGAAATTGCAG
AAGCCTACCTTGGGAAGACTGTTGCCAATGCCATTGTCACTGTACCAGCCTACTGTAATGACTCTTTGTGTCAGGCTACC
AAAGATGCTGGAACCATTGCTGGCCTCAATGTACTCAGAATCATCAACAAGCCAACTGCTGCTTATGTCTCAGATAAAAA
AGTTGGTGTGAAAGACATGTGTTAATCTTTGACTTAGGAGGTGGCACTTTTGATGTGTAAATCCTCACCACGGAAGATGG
AATCTTTGAGGTCAAATCTATAGATGGAGGCACTCACTTAGGTGGAGAAGACTTTGGCAATCAAATTTTTATTGCCGAGT
TCAAGCACAAGCATAAGAAGGACATCAGCGAGAACAAGAGGGCTGTTCGTCGCCTCCACACTGCTTTTGAACGTGCAAAG
CACACTCTATCTTCCAGCACCCAGGCCAGTACTGAGATTGATTCTCTCTACGAAGGATCTACTTCTATTCATCCATCACC
CGTGCCCGTTTGAAGAATTGAATGGTGACCTGTTCCATGGCACCCTGAACCCTGTGGAGAAAGCCCTTAGGGATTCCAAG
CTAGATGAGTCATAAATCCATGACATTCTCCTGGTGGGTGGTTCTATCAGTATTCCCAAGATTCGAAACTTCTTCATGAT
TTCTTCAGTGGAAAAGAATTGAACAAGACCATCAGTGCTGATTGCTTATGGTGCAGCTATACAGGCAGCTATCTTATCTG
GAGACAAATCAAAATGTTCAGGATTTACTGCTCTTGACACTCCTCTTTCCCTTGGTATTGAAACTGCTGGTGGAGTCATG
ACTGTCCTCATCAAGTACAATACTACCATTCCTACCAAGGAGACACAGACCTTCACAACCTACTCTGAGAACAACCCTGG
AGTACTCATTCACGTTTGTGAAGGTGAGAGTGCCATGACCAAGGATAACAACCTACTTGGCAAGTTTGAACTCACTGGCA
TACCTCCTGCACTCTGTGGTGCGCCTCAGATTGAAGTCATTTTTGCTATTTATGCCAACGGCATCCTCAGTGTCTCAGCT
GAGGATAAGAGTACTGGAAAAGAGAACAAGATTGCCATCACTAATGACAAGGGCCGCTTGAGTAATGAAGACATTGAGCA
TATGGTCTAGGACACTGAGAAGTACGAAGCTGAAGATGAGAAACAGAGGGACAAGATGTCCTCTAAGAATTCACTTGAAT
CCTATGCATTTAACATGAAAGGAACAGTTGAAGATGAAAAACTTCAAGGCAAGACCAATGATGAGGACAAACAA

ORF - retro_lafr_790 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.75 %
Parental protein coverage: 87.38 %
Number of stop codons detected: 7
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDA
M.K.PAVGIDLGT.YS.VGVFQ.GKVEIIANDQGNRTTPSY..F.D.E.LIGDA.KNQVAMNPTNTVFDA
RetrocopyMPKRPAVGIDLGTIYSHVGVFQLGKVEIIANDQGNRTTPSYTSFIDIE*LIGDARKNQVAMNPTNTVFDA
ParentalKRLIGRRFDDAVVQSDMKHWPFVVVNDAGRPKVQVEYK--GETKSFYPEEVSSMVLTKMKEIAEAYLGKT
K.L.G.RFDDAVVQSDMK.WPF....DAGRPKVQ.EYK..GETKSFYPEEVSSMVLTKMKEIAEAYLGKT
RetrocopyKCLTG*RFDDAVVQSDMKYWPFME*SDAGRPKVQIEYKDKGETKSFYPEEVSSMVLTKMKEIAEAYLGKT
ParentalVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGA-ERNVLIFDLGGGTFDV
V.NA.VTVPAY.NDS..QATKDAGTIAGLNVLRIIN.PTA...AY..DKKVG..ER.VLIFDLGGGTFDV
RetrocopyVANAIVTVPAYCNDSLCQATKDAGTIAGLNVLRIINKPTA---AYVSDKKVGV<ERHVLIFDLGGGTFDV
ParentalSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSS
.ILT.EDGIFEVKS..G.THLGGEDF.N.....FIAEFK.KHKKDISENKRAVRRL.TA.ERAK.TLSSS
Retrocopy*ILTTEDGIFEVKSIDGGTHLGGEDFGNQI---FIAEFKHKHKKDISENKRAVRRLHTAFERAKHTLSSS
ParentalTQASIEIDSLYEG-IDFYTSITRAR-FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPK
TQAS.EIDSLYEG.I.FY.SITRAR.FEELN.DLF.GTL.PVEKALRD.KLD.S.IHDI.LVGGS..IPK
RetrocopyTQASTEIDSLYEG<IYFYSSITRAR<FEELNGDLFHGTLNPVEKALRDSKLDES*IHDILLVGGSISIPK
ParentalIQKLLQDFFNGKELNKS-INPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLI
.......FF......K....P....AYGAA.QAAILSGDKS........LD.TPLSLGIETAGGVMTVLI
Retrocopy----IRNFFMISSVEKN*TRPSVLIAYGAAIQAAILSGDKSK-CSGFTALD-TPLSLGIETAGGVMTVLI
ParentalKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANG
K.NTTIPTK.TQTFTTYS.N.PGVLI.V.EGE.AMTKDNNLLGKFELTGIPPA..G.PQIEV.F.I.ANG
RetrocopyKYNTTIPTKETQTFTTYSENNPGVLIHVCEGESAMTKDNNLLGKFELTGIPPALCGAPQIEVIFAIYANG
ParentalILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVE
IL.VSA.DKSTGKENKI.ITNDKGRLS.EDIE.MV...EKY.AEDEKQRDK.SSKNSLESYAFNMK.TVE
RetrocopyILSVSAEDKSTGKENKIAITNDKGRLSNEDIEHMV*DTEKYEAEDEKQRDKMSSKNSLESYAFNMKGTVE
ParentalDEKLQGKISDEDKQ
DEKLQGK..DEDKQ
RetrocopyDEKLQGKTNDEDKQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_790 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 35 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
Anas platyrhynchos ENSAPLG000000106671 retrocopy
Bos taurus ENSBTAG000000131621 retrocopy
Canis familiaris ENSCAFG000000116663 retrocopies
Ciona intestinalis ENSCING000000096651 retrocopy
Callithrix jacchus ENSCJAG000000076485 retrocopies
Cavia porcellus ENSCPOG000000041693 retrocopies
Ciona savignyi ENSCSAVG000000085881 retrocopy
Dipodomys ordii ENSDORG000000154671 retrocopy
Equus caballus ENSECAG000000135102 retrocopies
Echinops telfairi ENSETEG000000109961 retrocopy
Ficedula albicollis ENSFALG000000058121 retrocopy
Felis catus ENSFCAG000000011326 retrocopies
Homo sapiens ENSG000001099718 retrocopies
Gallus gallus ENSGALG000000065121 retrocopy
Gorilla gorilla ENSGGOG000000083818 retrocopies
Loxodonta africana ENSLAFG00000030312 4 retrocopies
Meleagris gallopavo ENSMGAG000000019291 retrocopy
Myotis lucifugus ENSMLUG000000048343 retrocopies
Macaca mulatta ENSMMUG000000046967 retrocopies
Monodelphis domestica ENSMODG000000129582 retrocopies
Mustela putorius furoENSMPUG000000058109 retrocopies
Mus musculus ENSMUSG000000156568 retrocopies
Nomascus leucogenys ENSNLEG000000074198 retrocopies
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
Oreochromis niloticus ENSONIG000000047591 retrocopy
Pongo abelii ENSPPYG000000039879 retrocopies
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
Pan troglodytes ENSPTRG000000044045 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
Taeniopygia guttata ENSTGUG000000004911 retrocopy
Takifugu rubripes ENSTRUG000000052651 retrocopy
Tursiops truncatus ENSTTRG000000111396 retrocopies
Xiphophorus maculatus ENSXMAG000000016021 retrocopy



Copyright © RetrogeneDB 2014-2017